Alright, I think that it is there, but there are good reasons it is not used (not-warp capable, no armor, problems with re-attachment, Picard doesn't like it ...) - as you said Timo.
But I can understand your point. Timo could you please list some (let's say 3-4) examples where you think they ought to have mentioned/used the yacht?
A big support for your argument is the Galaxy-X refit in "All Good Things...". After all, the Phaser spinal lance would prohibit the use of the yacht if it were still (or at all) on board.